Refactor read_file.py as a class and minimize repetition of code

[abuzarmahmood]

[abuzarmahmood]

Summary of Suggestions and Changes

1. Identification of Relevant File:

   • File: /home/exouser/Desktop/blech_github_bot/repos/katzlabbrandeis/blech_clust/utils/read_file.py
   • Description: This module handles digital inputs and reads data from Intan format files, saving it into HDF5 format. It includes a class DigInHandler and several standalone functions for data processing.

2. Plan to Address the Issue:

   • Encapsulate standalone functions into a class structure.
   • Identify and abstract common patterns or repeated code segments into helper methods within the class.
   • Ensure the refactored code maintains the same functionality and output as the original.

3. Specific Changes Suggested:

   • Encapsulate Standalone Functions into a Class:

     • File: /home/exouser/Desktop/blech_github_bot/repos/katzlabbrandeis/blech_clust/utils/read_file.py
     • Lines: 238-387
     • Description: Create a new class, IntanDataHandler, to encapsulate the standalone functions. This class will manage the reading and processing of Intan format data.
     • Code Snippet:

       class IntanDataHandler:
           def __init__(self, hdf5_name, electrode_layout_frame):
               self.hdf5_name = hdf5_name
               self.electrode_layout_frame = electrode_layout_frame
       
           def read_traditional_intan(self, file_list):
               # Existing code from read_traditional_intan function
               ...
       
           def read_emg_channels(self):
               # Existing code from read_emg_channels function
               ...
       
           def read_electrode_channels(self):
               # Existing code from read_electrode_channels function
               ...
       
           def read_electrode_emg_channels_single_file(self, electrodes_list, num_recorded_samples, emg_channels):
               # Existing code from read_electrode_emg_channels_single_file function
               ...

   • Abstract Common Patterns into Helper Methods:

     • File: /home/exouser/Desktop/blech_github_bot/repos/katzlabbrandeis/blech_clust/utils/read_file.py
     • Lines: Various
     • Description: Identify repeated code segments, such as file reading and data processing, and abstract them into helper methods within the IntanDataHandler class.
     • Code Snippet:

       class IntanDataHandler:
           ...
       
           def _read_data_from_file(self, filename):
               return np.fromfile(filename, dtype=np.dtype('int16'))
       
           def _create_earray(self, group, array_name, atom):
               hf5 = tables.open_file(self.hdf5_name, 'r+')
               if os.path.join(group, array_name) not in hf5:
                   return hf5.create_earray(group, array_name, atom, (0,))
               else:
                   return hf5.get_node(group, array_name)
       
           # Use these helper methods in the existing functions
           ...

By implementing these changes, the code will be more organized, maintainable, and reduce repetition, making it easier to extend functionality in the future.

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This response was automatically generated by blech_bot using model gpt-4o

[abuzarmahmood]

[ develop_issue ]

[abuzarmahmood]

Created pull request: #554
Continue discussion there.

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This response was automatically generated by blech_bot using model gpt-4o